When Desmond discovers that the Baphomet Idol is hidden in the Vannacutt Psychiatric Institute for the Criminally Insane, he and his team, including Samuel, go to Ariel Wolfe's house and abduct her and Paul for Dr. Vannacutt's journal, which may help them find the Idol.
Samuel and the team then travel to the Vannacutt asylum, and while Desmond and the team go inside with Ariel, Samuel stays outside at the team's car with Paul to guard him. Eventually, when what appears to be Desmond tells Samuel over the radio to go into the facility, he and Paul enter the house and search inside for Desmond. When Paul and Samuel hear Kyle screaming from up in the lobby, the two meet up with Desmond there.
Desmond and Samuel argue over whether or not it was Desmond who ordered Samuel to come into the house, and Ariel claims that it is the house that Samuel heard. While the group argue over whether or not the house is alive, Samuel is lured off into the basement by a shadow, where he is attacked by the Nurse Ghost. The ghost straps Samuel down in a wheelchair and takes him to Dr. Vannacutt. Vannacutt surgically removes the still-alive Samuel's scalp, and, despite Samuel's pleas, he rips Samuel's brain from his skull, killing him.
After Samuel died, his soul presumably joined the other ghosts trapped in the house. However, it can also be presumed that Samuel's ghost was freed from the house just hours after his death when Ariel removed the Baphomet Idol from the facility.